Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 43V5N

Calculation Name: 4U7U-K-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4U7U

Chain ID: K

ChEMBL ID:

UniProt ID: Q46898

Base Structure: X-ray

Registration Date: 2023-06-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2548282.834301
FMO2-HF: Nuclear repulsion 2461598.825427
FMO2-HF: Total energy -86684.008873
FMO2-MP2: Total energy -86934.972422


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(K:1:MET)


Summations of interaction energy for fragment #1(K:1:MET)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-7.65-2.6272.337-2.59-4.769-0.007
Interaction energy analysis for fragmet #1(K:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.021
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3K3SER00.0200.0133.8201.5193.253-0.020-0.859-0.8550.001
4K4TYR0-0.028-0.0184.497-0.751-0.617-0.001-0.009-0.1230.000
5K5LEU00.0010.0059.2770.0600.0600.0000.0000.0000.000
6K6ILE0-0.043-0.01911.5160.0280.0280.0000.0000.0000.000
7K7LEU00.0290.01715.052-0.016-0.0160.0000.0000.0000.000
8K8ARG10.8790.93218.790-0.059-0.0590.0000.0000.0000.000
9K9LEU0-0.045-0.01421.630-0.017-0.0170.0000.0000.0000.000
10K10ALA00.0610.01824.1240.0110.0110.0000.0000.0000.000
11K11GLY00.0460.01927.354-0.009-0.0090.0000.0000.0000.000
12K12PRO0-0.0050.00931.0270.0050.0050.0000.0000.0000.000
13K13MET00.0170.00333.7530.0030.0030.0000.0000.0000.000
14K14GLN0-0.005-0.01226.678-0.011-0.0110.0000.0000.0000.000
15K15ALA0-0.0050.00330.6170.0040.0040.0000.0000.0000.000
16K16TRP00.0090.00825.671-0.015-0.0150.0000.0000.0000.000
17K17GLY0-0.003-0.00128.6780.0050.0050.0000.0000.0000.000
18K18GLN00.0260.00328.9510.0050.0050.0000.0000.0000.000
19K19PRO0-0.002-0.01430.170-0.003-0.0030.0000.0000.0000.000
20K20THR00.0050.01633.0080.0030.0030.0000.0000.0000.000
21K21PHE0-0.035-0.02235.468-0.005-0.0050.0000.0000.0000.000
22K22GLU-1-0.832-0.89739.009-0.018-0.0180.0000.0000.0000.000
23K23GLY00.0130.00240.620-0.002-0.0020.0000.0000.0000.000
24K24THR00.0240.00439.8060.0000.0000.0000.0000.0000.000
25K25ARG10.7870.88236.1780.0280.0280.0000.0000.0000.000
26K26PRO00.0470.01533.8620.0010.0010.0000.0000.0000.000
27K27THR0-0.0050.00830.675-0.007-0.0070.0000.0000.0000.000
28K28GLY00.0110.02428.4070.0050.0050.0000.0000.0000.000
29K29ARG10.9550.94627.122-0.040-0.0400.0000.0000.0000.000
30K30PHE00.0170.00920.5400.0120.0120.0000.0000.0000.000
31K31PRO0-0.035-0.00521.699-0.007-0.0070.0000.0000.0000.000
32K32THR00.0620.04222.174-0.001-0.0010.0000.0000.0000.000
33K33ARG10.7170.81815.9380.2490.2490.0000.0000.0000.000
34K34SER00.014-0.00221.090-0.011-0.0110.0000.0000.0000.000
35K35GLY0-0.027-0.00324.167-0.005-0.0050.0000.0000.0000.000
36K36LEU00.009-0.00118.270-0.003-0.0030.0000.0000.0000.000
37K37LEU0-0.0030.00218.957-0.009-0.0090.0000.0000.0000.000
38K38GLY0-0.0020.00221.861-0.007-0.0070.0000.0000.0000.000
39K39LEU0-0.036-0.01122.9120.0020.0020.0000.0000.0000.000
40K40LEU00.0390.01617.7840.0000.0000.0000.0000.0000.000
41K41GLY00.022-0.00222.460-0.005-0.0050.0000.0000.0000.000
42K42ALA0-0.049-0.00324.8590.0050.0050.0000.0000.0000.000
43K43CYS0-0.050-0.02824.2040.0090.0090.0000.0000.0000.000
44K44LEU00.0690.03221.5900.0020.0020.0000.0000.0000.000
45K45GLY0-0.043-0.01526.0510.0110.0110.0000.0000.0000.000
46K46ILE0-0.020-0.01324.5390.0010.0010.0000.0000.0000.000
47K47GLN0-0.042-0.00929.2090.0090.0090.0000.0000.0000.000
48K48ARG10.9450.94531.0420.0760.0760.0000.0000.0000.000
49K49ASP-1-0.873-0.93432.099-0.106-0.1060.0000.0000.0000.000
50K50ASP-1-0.773-0.82129.503-0.168-0.1680.0000.0000.0000.000
51K51THR00.024-0.02428.633-0.008-0.0080.0000.0000.0000.000
52K52SER0-0.007-0.00726.824-0.006-0.0060.0000.0000.0000.000
53K53SER0-0.029-0.04324.969-0.026-0.0260.0000.0000.0000.000
54K54LEU0-0.068-0.03123.758-0.015-0.0150.0000.0000.0000.000
55K55GLN0-0.052-0.03522.9160.0040.0040.0000.0000.0000.000
56K56ALA00.0300.02520.752-0.022-0.0220.0000.0000.0000.000
57K57LEU0-0.0050.00619.022-0.041-0.0410.0000.0000.0000.000
58K58SER0-0.035-0.02918.272-0.027-0.0270.0000.0000.0000.000
59K59GLU-1-0.855-0.91917.056-0.280-0.2800.0000.0000.0000.000
60K60SER0-0.013-0.00714.877-0.079-0.0790.0000.0000.0000.000
61K61VAL00.0020.00613.231-0.097-0.0970.0000.0000.0000.000
62K62GLN0-0.030-0.01011.010-0.034-0.0340.0000.0000.0000.000
63K63PHE00.011-0.00812.346-0.006-0.0060.0000.0000.0000.000
64K64ALA00.0090.00111.8760.0060.0060.0000.0000.0000.000
65K65VAL0-0.022-0.00513.8390.0180.0180.0000.0000.0000.000
66K66ARG10.8300.91316.818-0.216-0.2160.0000.0000.0000.000
67K67CYS0-0.053-0.02518.575-0.026-0.0260.0000.0000.0000.000
68K68ASP-1-0.748-0.83321.4200.1480.1480.0000.0000.0000.000
69K69GLU-1-0.881-0.93223.9560.0880.0880.0000.0000.0000.000
70K70LEU00.0040.01127.4320.0060.0060.0000.0000.0000.000
71K71ILE0-0.013-0.01629.4150.0010.0010.0000.0000.0000.000
72K72LEU00.0140.00032.048-0.002-0.0020.0000.0000.0000.000
73K73ASP-1-0.913-0.93435.2670.0490.0490.0000.0000.0000.000
74K74ASP-1-0.883-0.95334.7180.0720.0720.0000.0000.0000.000
75K75ARG10.8120.90135.792-0.065-0.0650.0000.0000.0000.000
76K76ARG10.8910.93728.550-0.121-0.1210.0000.0000.0000.000
77K77VAL00.000-0.00132.730-0.005-0.0050.0000.0000.0000.000
78K78SER0-0.009-0.00531.8780.0010.0010.0000.0000.0000.000
79K79VAL00.0150.01628.595-0.005-0.0050.0000.0000.0000.000
80K80THR0-0.0110.00032.021-0.002-0.0020.0000.0000.0000.000
81K81GLY00.000-0.00134.358-0.003-0.0030.0000.0000.0000.000
82K82LEU00.0120.01036.1500.0010.0010.0000.0000.0000.000
83K83ARG10.9480.96238.314-0.005-0.0050.0000.0000.0000.000
84K84ASP-1-0.863-0.92940.915-0.009-0.0090.0000.0000.0000.000
85K85TYR0-0.057-0.04642.625-0.002-0.0020.0000.0000.0000.000
86K86HIS00.0280.01941.775-0.002-0.0020.0000.0000.0000.000
87K87THR00.0130.00345.316-0.001-0.0010.0000.0000.0000.000
88K88VAL0-0.040-0.02945.638-0.002-0.0020.0000.0000.0000.000
89K89LEU00.0480.03248.8130.0010.0010.0000.0000.0000.000
90K90GLY00.0550.04152.009-0.001-0.0010.0000.0000.0000.000
91K91ALA0-0.080-0.03048.607-0.002-0.0020.0000.0000.0000.000
92K92ARG10.9470.96542.8270.0400.0400.0000.0000.0000.000
93K93GLU-1-0.811-0.88649.796-0.023-0.0230.0000.0000.0000.000
94K94ASP-1-0.826-0.89850.316-0.028-0.0280.0000.0000.0000.000
95K95TYR0-0.091-0.05743.159-0.002-0.0020.0000.0000.0000.000
96K96ARG10.9560.96947.9780.0380.0380.0000.0000.0000.000
97K97GLY00.0220.01750.8590.0020.0020.0000.0000.0000.000
98K98LEU0-0.006-0.02152.760-0.001-0.0010.0000.0000.0000.000
99K99LYS10.7860.90455.0250.0260.0260.0000.0000.0000.000
100K100SER00.0300.00053.596-0.001-0.0010.0000.0000.0000.000
101K101HIS0-0.015-0.01051.0370.0000.0000.0000.0000.0000.000
102K102GLU-1-0.900-0.94354.601-0.016-0.0160.0000.0000.0000.000
103K103THR00.017-0.02452.9940.0000.0000.0000.0000.0000.000
104K104ILE0-0.055-0.00147.0370.0000.0000.0000.0000.0000.000
105K105GLN00.0200.01348.0180.0010.0010.0000.0000.0000.000
106K106THR0-0.054-0.01742.541-0.002-0.0020.0000.0000.0000.000
107K107TRP00.0280.01642.5140.0010.0010.0000.0000.0000.000
108K108ARG10.8640.93138.2560.0220.0220.0000.0000.0000.000
109K109GLU-1-0.851-0.92435.8070.0030.0030.0000.0000.0000.000
110K110TYR0-0.032-0.01234.223-0.008-0.0080.0000.0000.0000.000
111K111LEU0-0.055-0.01928.6770.0040.0040.0000.0000.0000.000
112K112CYS0-0.014-0.01832.805-0.006-0.0060.0000.0000.0000.000
113K113ASP-1-0.845-0.92032.6030.0370.0370.0000.0000.0000.000
114K114ALA0-0.035-0.00328.0620.0070.0070.0000.0000.0000.000
115K115SER00.023-0.00224.970-0.012-0.0120.0000.0000.0000.000
116K116PHE0-0.003-0.01221.3950.0080.0080.0000.0000.0000.000
117K117THR0-0.014-0.02517.056-0.011-0.0110.0000.0000.0000.000
118K118VAL0-0.048-0.03015.9960.0160.0160.0000.0000.0000.000
119K119ALA00.0180.01111.3100.0110.0110.0000.0000.0000.000
120K120LEU0-0.018-0.01412.282-0.026-0.0260.0000.0000.0000.000
121K121TRP0-0.008-0.0197.8860.0840.0840.0000.0000.0000.000
122K122LEU00.0050.0059.5940.0940.0940.0000.0000.0000.000
123K123THR0-0.030-0.0228.549-0.285-0.2850.0000.0000.0000.000
124K124PRO00.008-0.0208.271-0.008-0.0080.0000.0000.0000.000
125K125HIS0-0.036-0.00710.5060.0170.0170.0000.0000.0000.000
126K126ALA0-0.0380.00412.9730.0780.0780.0000.0000.0000.000
127K127THR0-0.028-0.01414.6340.0250.0250.0000.0000.0000.000
128K128MET0-0.021-0.00216.5150.0350.0350.0000.0000.0000.000
129K129VAL00.022-0.00314.490-0.104-0.1040.0000.0000.0000.000
130K130ILE00.0660.02310.0580.0820.0820.0000.0000.0000.000
131K131SER00.0240.00814.1670.0700.0700.0000.0000.0000.000
132K132GLU-1-0.869-0.93516.288-0.332-0.3320.0000.0000.0000.000
133K133LEU0-0.008-0.00515.3540.0510.0510.0000.0000.0000.000
134K134GLU-1-0.926-0.96215.161-0.247-0.2470.0000.0000.0000.000
135K135LYS10.9500.96718.0260.2570.2570.0000.0000.0000.000
136K136ALA0-0.010-0.00221.0630.0260.0260.0000.0000.0000.000
137K137VAL0-0.022-0.02619.6350.0240.0240.0000.0000.0000.000
138K138LEU0-0.039-0.00919.7790.0230.0230.0000.0000.0000.000
139K139LYS10.8570.93423.4710.1360.1360.0000.0000.0000.000
140K140PRO00.0060.03126.223-0.009-0.0090.0000.0000.0000.000
141K141ARG10.9100.94527.5420.1450.1450.0000.0000.0000.000
142K142TYR0-0.027-0.00330.1120.0100.0100.0000.0000.0000.000
143K143THR0-0.014-0.02130.533-0.001-0.0010.0000.0000.0000.000
144K144PRO00.0390.03527.628-0.001-0.0010.0000.0000.0000.000
145K145TYR0-0.049-0.04128.7380.0050.0050.0000.0000.0000.000
146K146LEU00.0160.02326.194-0.007-0.0070.0000.0000.0000.000
147K147GLY00.0710.04528.5060.0070.0070.0000.0000.0000.000
148K148ARG10.7710.86029.8830.0140.0140.0000.0000.0000.000
149K149ARG10.9170.95233.2680.0640.0640.0000.0000.0000.000
150K150SER00.0110.00335.078-0.001-0.0010.0000.0000.0000.000
151K151CYS0-0.068-0.01432.3670.0060.0060.0000.0000.0000.000
152K152PRO00.0420.01232.016-0.004-0.0040.0000.0000.0000.000
153K153LEU0-0.0030.00726.3560.0020.0020.0000.0000.0000.000
154K154THR0-0.018-0.02230.160-0.003-0.0030.0000.0000.0000.000
155K155HIS0-0.024-0.02222.7270.0140.0140.0000.0000.0000.000
156K156PRO00.0030.00224.036-0.008-0.0080.0000.0000.0000.000
157K157LEU00.0430.03622.0490.0090.0090.0000.0000.0000.000
158K158PHE00.0250.00616.1840.0070.0070.0000.0000.0000.000
159K159LEU0-0.040-0.01117.7210.0120.0120.0000.0000.0000.000
160K160GLY00.030-0.00215.3460.0100.0100.0000.0000.0000.000
161K161THR0-0.023-0.00111.375-0.033-0.0330.0000.0000.0000.000
162K162CYS0-0.049-0.0068.7150.1340.1340.0000.0000.0000.000
163K163GLN00.030-0.0023.297-1.772-1.4900.015-0.119-0.1780.000
164K164ALA0-0.0280.0003.766-0.6510.0970.042-0.284-0.5060.001
165K165SER00.0470.0162.206-2.2470.0422.212-2.054-2.448-0.006
166K166ASP-1-0.888-0.9443.233-0.627-0.7910.0890.735-0.659-0.003
167K167PRO00.0410.0296.0150.2610.2610.0000.0000.0000.000
168K168GLN00.0390.0148.3800.1130.1130.0000.0000.0000.000
169K169LYS10.9530.9727.556-1.368-1.3680.0000.0000.0000.000
170K170ALA00.0390.0228.0280.0140.0140.0000.0000.0000.000
171K171LEU00.021-0.0019.636-0.160-0.1600.0000.0000.0000.000
172K172LEU0-0.068-0.04112.472-0.064-0.0640.0000.0000.0000.000
173K173ASN0-0.092-0.02410.086-0.059-0.0590.0000.0000.0000.000
174K174TYR00.0280.00712.307-0.113-0.1130.0000.0000.0000.000
175K175GLU-1-0.820-0.88116.9670.2280.2280.0000.0000.0000.000
176K176PRO0-0.065-0.04220.441-0.024-0.0240.0000.0000.0000.000
177K177VAL0-0.008-0.02117.7070.0090.0090.0000.0000.0000.000
178K178GLY00.005-0.00219.661-0.017-0.0170.0000.0000.0000.000
179K179GLY0-0.0180.00520.702-0.015-0.0150.0000.0000.0000.000
180K180ASP-1-0.866-0.93619.4610.1860.1860.0000.0000.0000.000
181K181ILE0-0.028-0.03313.752-0.007-0.0070.0000.0000.0000.000
182K182TYR0-0.0230.00016.824-0.001-0.0010.0000.0000.0000.000
183K183SER00.016-0.01810.631-0.045-0.0450.0000.0000.0000.000
184K184GLU-1-0.755-0.87212.562-0.237-0.2370.0000.0000.0000.000
185K185GLU-1-0.833-0.8735.422-1.367-1.3670.0000.0000.0000.000
186K186SER0-0.024-0.0019.7350.1280.1280.0000.0000.0000.000
187K187VAL00.0350.0158.359-0.028-0.0280.0000.0000.0000.000
188K188THR00.0280.0028.574-0.046-0.0460.0000.0000.0000.000
189K189GLY0-0.0180.00711.168-0.045-0.0450.0000.0000.0000.000
190K190HIS0-0.028-0.01713.184-0.082-0.0820.0000.0000.0000.000
191K191HIS00.0500.01715.057-0.043-0.0430.0000.0000.0000.000
192K192LEU0-0.040-0.00317.726-0.027-0.0270.0000.0000.0000.000
193K193LYS10.9160.94016.552-0.001-0.0010.0000.0000.0000.000
194K194PHE0-0.022-0.01119.7170.0040.0040.0000.0000.0000.000
195K195THR0-0.0160.00221.587-0.012-0.0120.0000.0000.0000.000
196K196ALA00.0170.01922.7010.0040.0040.0000.0000.0000.000
197K197ARG10.8950.92624.6530.0400.0400.0000.0000.0000.000
198K198ASP-1-0.792-0.88722.044-0.059-0.0590.0000.0000.0000.000
199K199GLU-1-0.778-0.89020.140-0.183-0.1830.0000.0000.0000.000
200K200PRO0-0.0130.01122.7670.0160.0160.0000.0000.0000.000
201K201MET00.0110.01224.969-0.011-0.0110.0000.0000.0000.000
202K202ILE00.0350.02123.5330.0090.0090.0000.0000.0000.000
203K203THR00.0030.00427.7630.0050.0050.0000.0000.0000.000
204K204LEU0-0.042-0.01930.2080.0080.0080.0000.0000.0000.000
205K205PRO00.0420.01131.5570.0010.0010.0000.0000.0000.000
206K206ARG10.8730.93231.0140.0750.0750.0000.0000.0000.000
207K207GLN00.0620.04531.2010.0100.0100.0000.0000.0000.000
208K208PHE0-0.013-0.00826.944-0.007-0.0070.0000.0000.0000.000
209K209ALA00.008-0.00125.5020.0100.0100.0000.0000.0000.000
210K210SER0-0.048-0.04124.942-0.004-0.0040.0000.0000.0000.000
211K211ARG10.8900.95016.6560.0840.0840.0000.0000.0000.000
212K212GLU-1-0.848-0.92219.0970.0190.0190.0000.0000.0000.000
213K213TRP0-0.058-0.01116.156-0.023-0.0230.0000.0000.0000.000
214K214TYR00.0340.01513.2650.0340.0340.0000.0000.0000.000
215K215VAL0-0.027-0.02015.6860.0030.0030.0000.0000.0000.000
216K216ILE0-0.033-0.01212.7940.0190.0190.0000.0000.0000.000
217K217LYS10.9520.97416.556-0.166-0.1660.0000.0000.0000.000
218K218GLY0-0.0090.01118.9120.0400.0400.0000.0000.0000.000